Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 192 bits (488), Expect = 1e-53 Identities = 130/331 (39%), Positives = 181/331 (54%), Gaps = 32/331 (9%) Query: 28 LLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVI 87 L+ + L LVVL + F LT ++ F S N M + QV L T VI Sbjct: 23 LIQKFAALGSLVVLIVAF-SLT-------SAAFFSVGNLMTVALQVTSIAYLGVAATCVI 74 Query: 88 LTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFSGLVMGM----VNGAMVALLNI 143 +T GIDLSVGSVLA++ G+ +L G IP+ + G+++G VNG V + + Sbjct: 75 ITGGIDLSVGSVLALA---GVAAALLVKAGVPIPVAMLGGMLVGAACGWVNGICVTRMGL 131 Query: 144 NAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGD----------------FLH 187 F+ TLG M RG A L G ++ +F +GNG F Sbjct: 132 PPFIATLGMMLVARGLA-LQITGARPVSGLGDAFGELGNGALFRISHIGADGFPDTVFPG 190 Query: 188 VPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFS 247 +P+ + + V + ++L +T LG HIYA+G N +AARL+G+ V V LF Y +SGL + Sbjct: 191 IPYPVVIMVVLFAAVSILLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLA 250 Query: 248 GLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNG 307 G G + SRL A N G YELDAIA+ V+GGTSLMGGVG+I GT +GA +IGV+ NG Sbjct: 251 GATGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNG 310 Query: 308 LTILGLSSFWQYVAKGAVIVLAVILDKWRQK 338 L + G+SSF Q + G VI+ V +D+ R + Sbjct: 311 LNMNGVSSFIQQIIIGVVILGTVWIDQLRNR 341 Lambda K H 0.324 0.138 0.417 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 318 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 344 Length of database: 343 Length adjustment: 29 Effective length of query: 315 Effective length of database: 314 Effective search space: 98910 Effective search space used: 98910 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory